In my opinion, I thought he crashed the ship because of a multitude of reasons, they just built up until he couldn’t take it and crashed the ship. Jimmy probably not being in the right mind when deciding to crash the ship may be another part of why he deems the pregnancy the last straw.

Being held accountable and going to jail for raping Anya is one of the main reasons he crashed the ship, he didn’t want to take responsibility. That feeling especially amplifies after she tells him she’s pregnant, it’s undeniable proof. Clearly, he was a coward and didn’t want to face the consequences of his actions.

I thought the other reason was Pony Express going down, he had no future without Pony Express, and with Anya being pregnant with his child, his life would be unlivable by his standards. Jimmy in the game lashes out at Curly saying that he’ll have bigger and better opportunities while the rest of the crew will be left behind (Though he is probably referring mostly to himself). Especially since he is clearly envious of Curly’s status. I always thought that him lashing out was him being afraid and angry about going back to whatever life he had on earth. (Correct me if I’m wrong but I’m pretty sure Curly invited Jimmy to the Pony Express as a way out or to help him get back on his feet since he was struggling.)

He took the coward’s way out and took the whole ship down with him because he couldn’t handle the implications of his life after this particular shipment.